Additional files
Additional Table 1. Quality of sequencing results
Additional Table 2. Clinical features of 10 familial RP cases whose strong variants were
detected by targeted resequencing
Additional Table 3. Clinical features of 7 sporadic RP cases whose strong variants were
detected by targeted resequencing
Additional Table 4. In silico prediction for nonsysnonymous variants
Additional Figure 1. Pedigrees of 10 familial cases whose strong variants were detected by
targeted re-sequencing
Additional Figure 2. Fundus photograph and optical coherence tomography of the interesting
cases
Additional Table 1. Quality data for targeted exome sequencing
Reads
Aligned sequence (Mb)
Mean (± s.d.)
31.9 (± 5.7)
Total reads
2,887,637 (± 452,554)
Aligned paired reads
2,803,425 (± 433,353)
Aligned singleton reads
9,272 (± 435)
% of bases covered to
≥x1
98.6 (± 0.7)
≥x10
96.5 (± 1.6)
≥x25
92.9 (± 3.6)
≥x50
85.0 (± 7.7)
≥x75
75.0 (± 12.0)
≥x100
64.1 (± 14.6)
Additional Table 2. Clinical features of 10 familial RP cases whose variants were detected by targeted resequencing
Family
Gene
Sex
Age (y)
F03
RP1
M
21
F04
RP2
M
6
F06
RP1
M
F07
F09
PRPF31
RHO
M
F
F10
KLHL7
F12
F13
XF1
XF3
Symptom onset
age (y)
Lens
VA (OD)
VA (OS)
0.7
0.8
4
0.1
0.02
40
35
1.2
1.2
33
49
10
7
0.7
LP
0.8
LP
F
34
23
0.6
0.6
RP2
M
52
4
Cat
LP
HM
RHO
TOPORS
PRPF31
M
F
M
52
33
46
16
13
8
PCL
HM
0.5
0.4
NLP
0.3
0.3
Cat
Cat
ERG
extinguished
only low response at 30 Hz
flicker
extinguished
extinguished
extinguished
extinguished rod response,
markedly reduced cone
response
Only the clinical features of the proband (indexed patients of the families) were described.
PCL: cataract operation was done; Cat: lens opacity (cataract)
VA: best corrected visual acuity (Snellen); OD: right eye; OS: left eye
NLP: no light perception; LP: light perception; HM: hand movement; FC: counting finger
ERG: standard electro-retinogram, ISCEV protocol
OCT: optical coherence tomography
PR: preserved photoreceptor inner and outer segment junction in the horizontal macular scan (OD/OS)
ERM: epiretinal membrane; CME: cystoid macular edema
GVF: Goldmann visual field test
The visual field test results between both eyes were nearly identical.
OCT
GVF
PR 1.8/1.6
mild superior field
constriction
PR -/-
mildly constricted
PR 2.9/3
10°~20°
PR 1.1/1
PR -/-
10° and temporal island
(-)
PR 1.2/1.3, ERM
10°
extinguished
PR -/-, ERM
extinguished
PR -/PR 1.2, CME
PR 0.9
5°
Additional Table 3. Clinical features of 7 sporadic RP cases whose variants were detected by targeted resequencing
Symptom
onset age (y)
Patient
Gene
Sex
Age (y)
430
PRPF31
M
42
432
PRPH2
M
28
6
436
PDE6B
F
24
438
USH2A
M
439
EYS
440
445
Cataract
VA (OD)
VA (OS)
ERG
1
0.9
mildly decreased
response
cat
NLP
0.4
extinguished
13
cat
1.2
1
58
15
cat
FC
FC
M
57
15
cat
0.6
0.5
EYS
F
37
30
0.4
0.5
PDE6B
M
60
3
0.2
0.02
PCL
PCL: cataract operation was done; Cat: lens opacity(cataract)
VA: best corrected visual acuity (Snellen); OD: right eye; OS: left eye
NLP: no light perception; LP: light perception; HM: hand movement; FC: counting finger
ERG: standard electro-retinogram, ISCEV protocol
OCT: optical coherence tomography
PR: preserved photoreceptor inner and outer segment junction in the horizontal macular scan (OD/OS)
ERM: epiretinal membrane; CME: cystoid macular edema
GVF: Goldmann visual field test
The visual field test result between both eyes were nearly identical in all cases, except in patient 432.
extinguished
OCT
rod
PR 5/5.6
PR -/-
GVF
paracentral
scotoma
OD) (-) OS) 5°
5°
5°~10°
extinguished
PR 3/2.6
5~10°
PR -/-
<5°
Additional Table 4. In silico prediction for nonsysnonymous variants
No
Gene
nucleotide
amino acid
Reference
Class
Polyphen2
SIFT
MutPred
F04
RP2
c.340T>C
p.C114R
novel
Ⅱ
Prob (1.000)
Dam
0.904 (0.0051)
F09
RHO
c.1040C>T
p.P347L
I
Prob (1.000)
Dam
0.811 (0.0462)
F10
KLHL7
c.458C>T
p.A153V
I
Prob (0.993)
Dam
0.943
F13
RHO
c.533A>G
p.Y178C
rs29001566
rs137853113,
11 Wen
rs104893776
I
Prob (1.000)
Dam
0.917
XF4, 450
USH2A
c.10246T>G
p.C3416G
13 Huang
I
Prob (0.999)
Dam
0.448
430
PRPF31
c.310G>A
p.E104K
Novel
Ⅱ
Prob (0.967)
Dam
0.745 (0.0198)
432
PRPH2
c.380A>G
p.E127G
Novel
Ⅱ
Ben (0.121)
Dam
0.54
435
EYS
c.7394C>G
p.T2465S
rs145184183
Ⅱ
Prob (0.990)
Tol
0.614 (0.0349)
436, 445
PDE6B
c.832C>T
p.H278Y
rs121918581
Ι
Prob (0.991)
Dam
0.929
438
USH2A
c.8885T>G
p.L2962R
Novel
Ⅱ
Prob (1.000)
Dam
0.752 (0.0126)
440
EYS
c.6557G>A
p.G2186E
10 Littink
Ι
Poss (0.946)
Dam
0.926
445
PDE6B
c.767T>A
p.I256N
Novel
Ⅱ
Prob (0.981)
Dam
0.793
450
USH2A
c.6683T>A
p.V2228E
rs117461552
Ⅱ
Poss (0.868)
Dam
0.437
No: family or patient identifier
Class: Classification of candidate variants in this study described in Table 1
Prob: probably damaging; Poss: possibly damaging; Ben: benign
Dam: damaging; Tol: tolerable
Additional Figure 1. Pedigrees of 10 familial cases whose strong variants were detected by targeted re-sequencing
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Additional figure 2. Fundus photograph and optical coherence tomography of the interesting
cases
(A-C) F04 family whose candidate variants was p.C114R in RP2, (A) Fundus photograph and
(B) OCT of IV-1 patient. He was a 6-year-old and his visual acuity was 20/200 (OD) and
20/1000 (OS). Although fundus appearance looks not so degenerated, the photoreceptor inner
segment and outer segment junction was not detectable using OCT. (C) Fundus photograph of
Ⅱ-2 patient who is grandfather of IV-1 patient. This showed severely degenerated retina. (DG) F12 family whose candidate variant was p.Ser187fs in RP2. (D) Fundus photograph and (E)
OCT of Ⅱ-16 patient who is hemizygote male. (F) Fundus photograph and (G) OCT of Ⅱ13 patient who is heterozygote female. Both Ⅱ-16 and Ⅱ-13 showed severely degenerated
retina compatible with RP. Other female member of this family showed variable expression of
RP. (H and I) F06 family whose candidate variant is p.Q766X in RP1. (H) Fundus photograph
and (I) OCT of Ⅲ-6 patient. She was 49 years old and had normal vision. Fundal appearance
looks almost normal except pigmentary retinal deposit seen at nasal peripheral portion. OCT
scan showed intact macular structure. (J and K) Sporadic patient 430. Candidate variant was
p.E104K in PRPF31. He was 42 years old. He had normal vision. Retinal degeneration is seen
outside the arcade at fundus photograph. The photoreceptor inner segment and outer segment
junction damage is only seen at periphery using OCT.
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